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Ok, found the problem. At line 174 of BeanDocUtils you do a Split using the file separator, that happens to be "\\" under Windows (that's why it works on Linux).

Replacing split(File.separator) with split(File.separator.replace("\\", "\\\\"))
does the trick.

It seems that beandoc users and Windows users have been two separate sets so far ;-)

Thanks for tracking that down aaime, but it's a bit surprising because there are several people running it on windows. I ran and tested 0.6.1 on windows myself and it was fine. No changes to BeanDocUtils were made (IIRC) in 0.6.2 (which wasn't tested fully on windows). I'll find a windows box tomorrow and check this out properly.